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- PDB-4zkt: Crystal structure of the progenitor M complex of Clostridium botu... -

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Basic information

Entry
Database: PDB / ID: 4zkt
TitleCrystal structure of the progenitor M complex of Clostridium botulinum type E neurotoxin
Components
  • Bontoxilysin A
  • Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH
KeywordsHydrolase/Toxin / BoNT/E-NTNHE hetero-dimer / acidic cluster / domain swap / progenitor complex / Hydrolase-Toxin complex
Function / homology
Function and homology information


negative regulation of neurotransmitter secretion / bontoxilysin / protein transmembrane transporter activity / : / metalloendopeptidase activity / toxin activity / zinc ion binding / extracellular region
Similarity search - Function
Nontoxic nonhaemagglutinin C-terminal / Nontoxic nonhaemagglutinin C-terminal / Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease ...Nontoxic nonhaemagglutinin C-terminal / Nontoxic nonhaemagglutinin C-terminal / Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Alpha-Beta Complex / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Bontoxilysin A / Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH / : / :
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsEswaramoorthy, S. / Swaminathan, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA) United States
CitationJournal: Sci Rep / Year: 2015
Title: Molecular Assembly of Clostridium botulinum progenitor M complex of type E.
Authors: Eswaramoorthy, S. / Sun, J. / Li, H. / Singh, B.R. / Swaminathan, S.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bontoxilysin A
C: Bontoxilysin A
E: Bontoxilysin A
B: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH
D: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH
F: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)843,0279
Polymers842,8316
Non-polymers1963
Water0
1
A: Bontoxilysin A
B: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,0093
Polymers280,9442
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-55 kcal/mol
Surface area101440 Å2
MethodPISA
2
C: Bontoxilysin A
D: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,0093
Polymers280,9442
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-55 kcal/mol
Surface area101360 Å2
MethodPISA
3
E: Bontoxilysin A
F: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,0093
Polymers280,9442
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-55 kcal/mol
Surface area101180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.601, 192.601, 286.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E
14B
24D
15B
25F
16D
26F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYSAA2 - 12522 - 1252
21PROPROLYSLYSCB2 - 12522 - 1252
12PROPROLYSLYSAA2 - 12522 - 1252
22PROPROLYSLYSEC2 - 12522 - 1252
13PROPROLYSLYSCB2 - 12522 - 1252
23PROPROLYSLYSEC2 - 12522 - 1252
14LYSLYSLEULEUBD2 - 11602 - 1160
24LYSLYSLEULEUDE2 - 11602 - 1160
15LYSLYSLEULEUBD2 - 11602 - 1160
25LYSLYSLEULEUFF2 - 11602 - 1160
16LYSLYSLEULEUDE2 - 11602 - 1160
26LYSLYSLEULEUFF2 - 11602 - 1160

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Bontoxilysin A


Mass: 143990.359 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Clostridium botulinum (strain Alaska E43 / Type E3) (bacteria)
Strain: Alaska E43 / Type E3
References: UniProt: B2V3U7, UniProt: A0A0X1KH89*PLUS, bontoxilysin
#2: Protein Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH


Mass: 136953.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Clostridium botulinum (strain Alaska E43 / Type E3) (bacteria)
Strain: Alaska E43 / Type E3 / References: UniProt: B2V3U8, UniProt: A0A0X1KH90*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67 % / Description: Three hetero-dimers per asymmetric unit
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 5.0ul sample was equilibrated against 600ul of 6 - 8% PEG 4000 and 0.1M sodium acetate of pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 165586 / % possible obs: 69.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 110.6 Å2 / Net I/σ(I): 2.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFZ, 3V0A

3ffz

3v0a


Resolution: 3.05→49.3 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.872 / SU B: 38.792 / SU ML: 0.597 / Cross valid method: THROUGHOUT / ESU R Free: 0.762 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32083 1334 1 %RANDOM
Rwork0.24338 ---
obs0.24415 133607 59.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 134.999 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å21.03 Å20 Å2
2--1.03 Å20 Å2
3----3.33 Å2
Refinement stepCycle: 1 / Resolution: 3.05→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56949 0 3 0 56952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0258077
X-RAY DIFFRACTIONr_bond_other_d0.0050.0254825
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.94378768
X-RAY DIFFRACTIONr_angle_other_deg0.943125793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.84156987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4225.9622994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7341510098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.00115150
X-RAY DIFFRACTIONr_chiral_restr0.0730.28820
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0266846
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0213842
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it12.4912.48428128
X-RAY DIFFRACTIONr_mcbond_other12.48812.48428127
X-RAY DIFFRACTIONr_mcangle_it19.91418.63435055
X-RAY DIFFRACTIONr_mcangle_other19.91418.63435056
X-RAY DIFFRACTIONr_scbond_it12.95814.20329949
X-RAY DIFFRACTIONr_scbond_other12.95714.20329950
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other21.83120.70443714
X-RAY DIFFRACTIONr_long_range_B_refined30.73170663
X-RAY DIFFRACTIONr_long_range_B_other30.73170664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A78703
12C78703
21A78715
22E78715
31C78710
32E78710
41B70289
42D70289
51B70269
52F70269
61D70301
62F70301
LS refinement shellResolution: 3.05→3.133 Å
RfactorNum. reflection% reflection
Rwork0.673 3 -
Rfree-0 -
obs--0.02 %

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